Ah interesting, I suspected that there was a good reason behind it all 
I use a theme called RhinoUI by ui4rhino
My own icons are alright because I made them for a dark bg from start. But for some reason he decided to do his icons this way and let rhino invert them.
They are all SVG. (but embedded in a dll) So I guess I’ll have to export them one at a time to invert them in illustrator (?) (Hope there’s a better way)